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Seddon AR, Damiano OM, Hampton MB, Stevens AJ. Widespread genomic de novo DNA methylation occurs following CD8 + T cell activation and proliferation. Epigenetics 2024; 19:2367385. [PMID: 38899429 PMCID: PMC11195465 DOI: 10.1080/15592294.2024.2367385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
This research investigates the intricate dynamics of DNA methylation in the hours following CD8+ T cell activation, during a critical yet understudied temporal window. DNA methylation is an epigenetic modification central to regulation of gene expression and directing immune responses. Our investigation spanned 96-h post-activation and unveils a nuanced tapestry of global and site-specific methylation changes. We identified 15,626 significant differentially methylated CpGs spread across the genome, with the most significant changes occurring within the genes ADAM10, ICA1, and LAPTM5. While many changes had modest effect sizes, approximately 120 CpGs exhibited a log2FC above 1.5, with cell activation and proliferation pathways the most affected. Relatively few of the differentially methylated CpGs occurred along adjacent gene regions. The exceptions were seven differentially methylated gene regions, with the Human T cell Receptor Alpha Joining Genes demonstrating consistent methylation change over a 3kb window. We also investigated whether an inflammatory environment could alter DNA methylation during activation, with proliferating cells exposed to the oxidant glycine chloramine. No substantial differential methylation was observed in this context. The temporal perspective of early activation adds depth to the evolving field of epigenetic immunology, offering insights with implications for therapeutic innovation and expanding our understanding of epigenetic modulation in immune function.
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Affiliation(s)
- Annika R. Seddon
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago, Christchurch, New Zealand
| | - Olivia M. Damiano
- Department of Pathology and Molecular Medicine, Genetics and Epigenetics Research Group, University of Otago, Wellington, New Zealand
| | - Mark B. Hampton
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago, Christchurch, New Zealand
| | - Aaron J. Stevens
- Department of Pathology and Molecular Medicine, Genetics and Epigenetics Research Group, University of Otago, Wellington, New Zealand
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2
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Sacristán C, Youngblood BA, Lu P, Bally APR, Xu JX, McGary K, Hewitt SL, Boss JM, Skok JA, Ahmed R, Dustin ML. Chronic viral infection alters PD-1 locus subnuclear localization in cytotoxic CD8 + T cells. Cell Rep 2024; 43:114547. [PMID: 39083377 DOI: 10.1016/j.celrep.2024.114547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/15/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
During chronic infection, virus-specific CD8+ cytotoxic T lymphocytes (CTLs) progressively lose their ability to mount effective antiviral responses. This "exhaustion" is coupled to persistent upregulation of inhibitory receptor programmed death-1 (PD-1) (Pdcd1)-key in suppressing antiviral CTL responses. Here, we investigate allelic Pdcd1 subnuclear localization and transcription during acute and chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Pdcd1 alleles dissociate from transcriptionally repressive chromatin domains (lamin B) in virus-specific exhausted CTLs but not in naive or effector CTLs. Relative to naive CTLs, nuclear positioning and Pdcd1-lamina dissociation in exhausted CTLs reflect loss of Pdcd1 promoter methylation and greater PD-1 upregulation, although a direct correlation is not observed in effector cells, 8 days post-infection. Genetic deletion of B lymphocyte-induced maturation protein 1 (Blimp-1) enhances Pdcd1-lamina dissociation in effector CTLs, suggesting that Blimp-1 contributes to maintaining Pdcd1 localization to repressive lamina. Our results identify mechanisms governing Pdcd1 subnuclear localization and the broader role of chromatin dynamics in T cell exhaustion.
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Affiliation(s)
- Catarina Sacristán
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Ben A Youngblood
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA; Immunology Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Peiyuan Lu
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Alexander P R Bally
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Jean Xiaojin Xu
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Katelyn McGary
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Susannah L Hewitt
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Jeremy M Boss
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Rafi Ahmed
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Michael L Dustin
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA; The Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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3
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Mann BT, Sanz M, Clohosey M, Langlands K, Chitrakar A, Moreno C, Vitalle J, Iannone MA, Ruiz-Mateos E, Deleage C, Siegel M, Soriano-Sarabia N. Dual role of circulating and mucosal Vδ1 T cells in the control of and contribution to persistent HIV-1 infection. RESEARCH SQUARE 2024:rs.3.rs-4784403. [PMID: 39149467 PMCID: PMC11326412 DOI: 10.21203/rs.3.rs-4784403/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Curative strategies for human immunodeficiency virus (HIV-1) infection are hindered by incomplete characterization of the latent reservoir and limited enhancement of anti-HIV immune responses. In this study, we identified a novel dual role for peripheral and tissue-resident Vδ1 T cells within the gastrointestinal mucosa of virally suppressed people with HIV. Phenotypic analyses identified an increased frequency of highly differentiated, cytotoxic effector Vδ1 T cells that exerted potent inhibition of HIV-1 replication in vitro coinciding with direct increases in cytolytic function. Conversely, we detected an enrichment of HIV-1 DNA in tissue-resident CD4+Vδ1 T cells in situ. Despite low CD4 expression, we found circulating Vδ1 T cells also contained HIV-1 DNA which was replication-competent. We show that TCR-mediated activation of peripheral Vδ1 T cells induced de novo upregulation of CD4 providing a plausible mechanism for increased permissibility to infection. These findings highlight juxtaposing roles for Vδ1 T cells in HIV-1 persistence including significant contribution to tissue reservoirs.
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Affiliation(s)
- Brendan T Mann
- Departments of Microbiology, Immunology and Tropical Medicine and The George Washington University, Washington, DC, USA
| | - Marta Sanz
- Departments of Microbiology, Immunology and Tropical Medicine and The George Washington University, Washington, DC, USA
| | - Matthew Clohosey
- Departments of UNC-HIV Cure Center, Department of Medicine and University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kayley Langlands
- Departments of Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Alisha Chitrakar
- Departments of Microbiology, Immunology and Tropical Medicine and The George Washington University, Washington, DC, USA
| | - Carles Moreno
- Departments of Microbiology, Immunology and Tropical Medicine and The George Washington University, Washington, DC, USA
| | - Joana Vitalle
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Marie Anne Iannone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Marc Siegel
- Departments of Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Natalia Soriano-Sarabia
- Departments of Microbiology, Immunology and Tropical Medicine and The George Washington University, Washington, DC, USA
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4
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Jia W, Li N, Wang J, Gong X, Ouedraogo SY, Wang Y, Zhao J, Grech G, Chen L, Zhan X. Immune-related gene methylation prognostic instrument for stratification and targeted treatment of ovarian cancer patients toward advanced 3PM approach. EPMA J 2024; 15:375-404. [PMID: 38841623 PMCID: PMC11148001 DOI: 10.1007/s13167-024-00359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/07/2024] [Indexed: 06/07/2024]
Abstract
Background DNA methylation is an important mechanism in epigenetics, which can change the transcription ability of genes and is closely related to the pathogenesis of ovarian cancer (OC). We hypothesize that DNA methylation is significantly different in OCs compared to controls. Specific DNA methylation status can be used as a biomarker of OC, and targeted drugs targeting these methylation patterns and DNA methyltransferase may have better therapeutic effects. Studying the key DNA methylation sites of immune-related genes (IRGs) in OC patients and studying the effects of these methylation sites on the immune microenvironment may provide a new method for further exploring the pathogenesis of OC, realizing early detection and effective monitoring of OC, identifying effective biomarkers of DNA methylation subtypes and drug targets, improving the efficacy of targeted drugs or overcoming drug resistance, and better applying it to predictive diagnosis, prevention, and personalized medicine (PPPM; 3PM) of OC. Method Hypermethylated subtypes (cluster 1) and hypomethylated subtypes (cluster 2) were established in OCs based on the abundance of different methylation sites in IRGs. The differences in immune score, immune checkpoints, immune cells, and overall survival were analyzed between different methylation subtypes in OC samples. The significant pathways, gene ontology (GO), and protein-protein interaction (PPI) network of the identified methylation sites in IRGs were enriched. In addition, the immune-related methylation signature was constructed with multiple regression analysis. A methylation site model based on IRGs was constructed and verified. Results A total of 120 IRGs with 142 differentially methylated sites (DMSs) were identified. The DMSs were clustered into a high-level methylation group (cluster 1) and a low-level methylation group (cluster 2). The significant pathways and GO analysis showed many immune-related and cancer-associated enrichments. A methylation site signature based on IRGs was constructed, including RORC|cg25112191, S100A13|cg14467840, TNF|cg04425624, RLN2|cg03679581, and IL1RL2|cg22797169. The methylation sites of all five genes showed hypomethylation in OC, and there were statistically significant differences among RORC|cg25112191, S100A13|cg14467840, and TNF|cg04425624 (p < 0.05). This prognostic model based on low-level methylation and high-level methylation groups was significantly linked to the immune microenvironment as well as overall survival in OC. Conclusions This study provided different methylation subtypes for OC patients according to the methylation sites of IRGs. In addition, it helps establish a relationship between methylation and the immune microenvironment, which showed specific differences in biological signaling pathways, genomic changes, and immune mechanisms within the two subgroups. These data provide ones to deeply understand the mechanism of immune-related methylation genes on the occurrence and development of OC. The methylation-site signature is also to establish new possibilities for OC therapy. These data are a precious resource for stratification and targeted treatment of OC patients toward an advanced 3PM approach. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00359-3.
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Affiliation(s)
- Wenshuang Jia
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Na Li
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Jingjing Wang
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Xiaoxia Gong
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Serge Yannick Ouedraogo
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Yan Wang
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
- Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117 People’s Republic of China
| | - Junkai Zhao
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
| | - Godfrey Grech
- Department of Pathology, University of Malta, Msida, Malta
| | - Liang Chen
- Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117 People’s Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People’s Republic of China
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Singh V, Nandi S, Ghosh A, Adhikary S, Mukherjee S, Roy S, Das C. Epigenetic reprogramming of T cells: unlocking new avenues for cancer immunotherapy. Cancer Metastasis Rev 2024; 43:175-195. [PMID: 38233727 DOI: 10.1007/s10555-024-10167-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
T cells, a key component of cancer immunotherapy, undergo a variety of histone modifications and DNA methylation changes since their bone marrow progenitor stages before developing into CD8+ and CD4+ T cells. These T cell types can be categorized into distinct subtypes based on their functionality and properties, such as cytotoxic T cells (Tc), helper T cells (Th), and regulatory T cells (Treg) as subtypes for CD8+ and CD4+ T cells. Among these, the CD4+ CD25+ Tregs potentially contribute to cancer development and progression by lowering T effector (Teff) cell activity under the influence of the tumor microenvironment (TME). This contributes to the development of therapeutic resistance in patients with cancer. Subsequently, these individuals become resistant to monoclonal antibody therapy as well as clinically established immunotherapies. In this review, we delineate the different epigenetic mechanisms in cancer immune response and its involvement in therapeutic resistance. Furthermore, the possibility of epi-immunotherapeutic methods based on histone deacetylase inhibitors and histone methyltransferase inhibitors are under investigation. In this review we highlight EZH2 as the principal driver of cancer cell immunoediting and an immune escape regulator. We have addressed in detail how understanding T cell epigenetic regulation might bring unique inventive strategies to overcome drug resistance and increase the efficacy of cancer immunotherapy.
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Affiliation(s)
- Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Aritra Ghosh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Indian Institute of Science Education and Research, Kolkata, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Homi Bhabha National Institute, Mumbai, 400094, India.
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6
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Almojil D, Diawara A, Soulama I, Dieng MM, Manikandan V, Sermé SS, Sombié S, Diarra A, Barry A, Coulibaly SA, Sirima SB, Idaghdour Y. Impact of Plasmodium falciparum infection on DNA methylation of circulating immune cells. Front Genet 2023; 14:1197933. [PMID: 37470040 PMCID: PMC10352500 DOI: 10.3389/fgene.2023.1197933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 07/21/2023] Open
Abstract
The regulation of immune cell responses to infection is a complex process that involves various molecular mechanisms, including epigenetic regulation. DNA methylation has been shown to play central roles in regulating gene expression and modulating cell response during infection. However, the nature and extent to which DNA methylation is involved in the host immune response in human malaria remains largely unknown. Here, we present a longitudinal study investigating the temporal dynamics of genome-wide in vivo DNA methylation profiles using 189 MethylationEPIC 850 K profiles from 66 children in Burkina Faso, West Africa, sampled three times: before infection, during symptomatic parasitemia, and after malaria treatment. The results revealed major changes in the DNA methylation profiles of children in response to both Plasmodium falciparum infection and malaria treatment, with widespread hypomethylation of CpGs upon infection (82% of 6.8 K differentially methylated regions). We document a remarkable reversal of CpG methylation profiles upon treatment to pre-infection states. These changes implicate divergence in core immune processes, including the regulation of lymphocyte, neutrophil, and myeloid leukocyte function. Integrative DNA methylation-mRNA analysis of a top differentially methylated region overlapping the pro-inflammatory gene TNF implicates DNA methylation of TNF cis regulatory elements in the molecular mechanisms of TNF regulation in human malaria. Our results highlight a central role of epigenetic regulation in mounting the host immune response to P. falciparum infection and in response to malaria treatment.
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Affiliation(s)
- Dareen Almojil
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Aïssatou Diawara
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Issiaka Soulama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Mame Massar Dieng
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Vinu Manikandan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samuel S. Sermé
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Salif Sombié
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Amidou Diarra
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Aissata Barry
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | - Sodiomon B. Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Teghanemt A, Misel-Wuchter K, Heath J, Thurman A, Pulipati P, Dixit G, Geesala R, Meyerholz DK, Maretzky T, Pezzulo A, Issuree PD. DNA demethylation fine-tunes IL-2 production during thymic regulatory T cell differentiation. EMBO Rep 2023; 24:e55543. [PMID: 36880575 PMCID: PMC10157375 DOI: 10.15252/embr.202255543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Regulatory T (T reg) cells developing in the thymus are essential to maintain tolerance and prevent fatal autoimmunity in mice and humans. Expression of the T reg lineage-defining transcription factor FoxP3 is critically dependent upon T cell receptor (TCR) and interleukin-2 (IL-2) signaling. Here, we report that ten-eleven translocation (Tet) enzymes, which are DNA demethylases, are required early during double-positive (DP) thymic T cell differentiation and prior to the upregulation of FoxP3 in CD4 single-positive (SP) thymocytes, to promote Treg differentiation. We show that Tet3 selectively controls the development of CD25- FoxP3lo CD4SP Treg cell precursors in the thymus and is critical for TCR-dependent IL-2 production, which drive chromatin remodeling at the FoxP3 locus as well as other Treg-effector gene loci in an autocrine/paracrine manner. Together, our results demonstrate a novel role for DNA demethylation in regulating the TCR response and promoting Treg cell differentiation. These findings highlight a novel epigenetic pathway to promote the generation of endogenous Treg cells for mitigation of autoimmune responses.
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Affiliation(s)
- Athmane Teghanemt
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Kara Misel-Wuchter
- Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Molecular Medicine Graduate Program, Iowa City, IA, USA
| | - Jace Heath
- Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Immunology Graduate Program, Iowa City, IA, USA
| | - Andrew Thurman
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Priyanjali Pulipati
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Garima Dixit
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ramasatya Geesala
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | | | - Thorsten Maretzky
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Alejandro Pezzulo
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Priya D Issuree
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Molecular Medicine Graduate Program, Iowa City, IA, USA.,Immunology Graduate Program, Iowa City, IA, USA
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8
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Li S. Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns. Cancer Treat Res 2023; 190:375-393. [PMID: 38113008 DOI: 10.1007/978-3-031-45654-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Tumor cells evolve through space and time, generating genetically and phenotypically diverse cancer cell populations that are continually subjected to the selection pressures of their microenvironment and cancer treatment.
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Affiliation(s)
- Sheng Li
- The Jackson Laboratory for Genomic Medicine and Cancer Center, Farmington, USA.
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9
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Zatterale F, Raciti GA, Prevenzano I, Leone A, Campitelli M, De Rosa V, Beguinot F, Parrillo L. Epigenetic Reprogramming of the Inflammatory Response in Obesity and Type 2 Diabetes. Biomolecules 2022; 12:biom12070982. [PMID: 35883538 PMCID: PMC9313117 DOI: 10.3390/biom12070982] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
For the past several decades, the prevalence of obesity and type 2 diabetes (T2D) has continued to rise on a global level. The risk contributing to this pandemic implicates both genetic and environmental factors, which are functionally integrated by epigenetic mechanisms. While these conditions are accompanied by major abnormalities in fuel metabolism, evidence indicates that altered immune cell functions also play an important role in shaping of obesity and T2D phenotypes. Interestingly, these events have been shown to be determined by epigenetic mechanisms. Consistently, recent epigenome-wide association studies have demonstrated that immune cells from obese and T2D individuals feature specific epigenetic profiles when compared to those from healthy subjects. In this work, we have reviewed recent literature reporting epigenetic changes affecting the immune cell phenotype and function in obesity and T2D. We will further discuss therapeutic strategies targeting epigenetic marks for treating obesity and T2D-associated inflammation.
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Affiliation(s)
- Federica Zatterale
- Department of Translational Medical Science, Federico II University of Naples, 80131 Naples, Italy; (F.Z.); (G.A.R.); (I.P.); (A.L.); (M.C.)
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
| | - Gregory Alexander Raciti
- Department of Translational Medical Science, Federico II University of Naples, 80131 Naples, Italy; (F.Z.); (G.A.R.); (I.P.); (A.L.); (M.C.)
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
| | - Immacolata Prevenzano
- Department of Translational Medical Science, Federico II University of Naples, 80131 Naples, Italy; (F.Z.); (G.A.R.); (I.P.); (A.L.); (M.C.)
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
| | - Alessia Leone
- Department of Translational Medical Science, Federico II University of Naples, 80131 Naples, Italy; (F.Z.); (G.A.R.); (I.P.); (A.L.); (M.C.)
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
| | - Michele Campitelli
- Department of Translational Medical Science, Federico II University of Naples, 80131 Naples, Italy; (F.Z.); (G.A.R.); (I.P.); (A.L.); (M.C.)
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
| | - Veronica De Rosa
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
| | - Francesco Beguinot
- Department of Translational Medical Science, Federico II University of Naples, 80131 Naples, Italy; (F.Z.); (G.A.R.); (I.P.); (A.L.); (M.C.)
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
- Correspondence: (F.B.); (L.P.); Tel.: +39-081-746-3248 (F.B.); +39-081-746-3045 (L.P.)
| | - Luca Parrillo
- Department of Translational Medical Science, Federico II University of Naples, 80131 Naples, Italy; (F.Z.); (G.A.R.); (I.P.); (A.L.); (M.C.)
- URT Genomic of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy;
- Correspondence: (F.B.); (L.P.); Tel.: +39-081-746-3248 (F.B.); +39-081-746-3045 (L.P.)
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10
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Papadogkonas G, Papamatheakis DA, Spilianakis C. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. Front Immunol 2022; 13:921375. [PMID: 35812421 PMCID: PMC9257000 DOI: 10.3389/fimmu.2022.921375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling developmentally essential gene sets. The core of transcription and epigenetic regulation is formulated by different epigenetic modifications determining gene expression. Apart from “classic” epigenetic modifications, 3D chromatin architecture is also purported to exert fundamental roles in gene regulation. Chromatin conformation both facilitates cell-specific factor binding at specified regions and is in turn modified as such, acting synergistically. The interplay between global and tissue-specific protein factors dictates the epigenetic landscape of T and innate lymphoid cell (ILC) lineages. The expression of global genome organizers such as CTCF, YY1, and the cohesin complexes, closely cooperate with tissue-specific factors to exert cell type-specific gene regulation. Special AT-rich binding protein 1 (SATB1) is an important tissue-specific genome organizer and regulator controlling both long- and short-range chromatin interactions. Recent indications point to SATB1’s cooperation with the aforementioned factors, linking global to tissue-specific gene regulation. Changes in 3D genome organization are of vital importance for proper cell development and function, while disruption of this mechanism can lead to severe immuno-developmental defects. Newly emerging data have inextricably linked chromatin architecture deregulation to tissue-specific pathophysiological phenotypes. The combination of these findings may shed light on the mechanisms behind pathological conditions.
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Affiliation(s)
- George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
- *Correspondence: Charalampos Spilianakis,
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11
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Wei K, Jiang P, Zhao J, Jin Y, Zhang R, Chang C, Xu L, Xu L, Shi Y, Guo S, He D. Biomarkers to Predict DMARDs Efficacy and Adverse Effect in Rheumatoid Arthritis. Front Immunol 2022; 13:865267. [PMID: 35418971 PMCID: PMC8995470 DOI: 10.3389/fimmu.2022.865267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 12/28/2022] Open
Abstract
Rheumatoid arthritis (RA), one of the most common immune system diseases, mainly affects middle-aged and elderly individuals and has a serious impact on the quality of life of patients. Pain and disability caused by RA are significant symptoms negatively affecting patients, and they are especially seen when inappropriate treatment is administered. Effective therapeutic strategies have evolved over the past few decades, with many new disease-modifying antirheumatic drugs (DMARDs) being used in the clinic. Owing to the breakthrough in the treatment of RA, the symptoms of patients who could not be treated effectively in the past few years have been relieved. However, some patients complain about symptoms that have not been reported, implying that there are still some limitations in the RA treatment and evaluation system. In recent years, biomarkers, an effective means of diagnosing and evaluating the condition of patients with RA, have gradually been used in clinical practice to evaluate the therapeutic effect of RA, which is constantly being improved for accurate application of treatment in patients with RA. In this article, we summarize a series of biomarkers that may be helpful in evaluating the therapeutic effect and improving the efficiency of clinical treatment for RA. These efforts may also encourage researchers to devote more time and resources to the study and application of biomarkers, resulting in a new evaluation system that will reduce the inappropriate use of DMARDs, as well as patients’ physical pain and financial burden.
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Affiliation(s)
- Kai Wei
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Ping Jiang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Jianan Zhao
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yehua Jin
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Runrun Zhang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China.,The Second Affiliated Hospital of the Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cen Chang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Lingxia Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Linshuai Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yiming Shi
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Shicheng Guo
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
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12
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CD4 expression in effector T cells depends on DNA demethylation over a developmentally established stimulus-responsive element. Nat Commun 2022; 13:1477. [PMID: 35304452 PMCID: PMC8933563 DOI: 10.1038/s41467-022-28914-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 02/16/2022] [Indexed: 12/17/2022] Open
Abstract
The epigenetic patterns that are established during early thymic development might determine mature T cell physiology and function, but the molecular basis and topography of the genetic elements involved are not fully known. Here we show, using the Cd4 locus as a paradigm for early developmental programming, that DNA demethylation during thymic development licenses a novel stimulus-responsive element that is critical for the maintenance of Cd4 gene expression in effector T cells. We document the importance of maintaining high CD4 expression during parasitic infection and show that by driving transcription, this stimulus-responsive element allows for the maintenance of histone H3K4me3 levels during T cell replication, which is critical for preventing de novo DNA methylation at the Cd4 promoter. A failure to undergo epigenetic programming during development leads to gene silencing during effector T cell replication. Our study thus provides evidence of early developmental events shaping the functional fitness of mature effector T cells.
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13
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Romano R, Cillo F, Moracas C, Pignata L, Nannola C, Toriello E, De Rosa A, Cirillo E, Coppola E, Giardino G, Brunetti-Pierri N, Riccio A, Pignata C. Epigenetic Alterations in Inborn Errors of Immunity. J Clin Med 2022; 11:1261. [PMID: 35268351 PMCID: PMC8910960 DOI: 10.3390/jcm11051261] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 02/07/2023] Open
Abstract
The epigenome bridges environmental factors and the genome, fine-tuning the process of gene transcription. Physiological programs, including the development, maturation and maintenance of cellular identity and function, are modulated by intricate epigenetic changes that encompass DNA methylation, chromatin remodeling, histone modifications and RNA processing. The collection of genome-wide DNA methylation data has recently shed new light into the potential contribution of epigenetics in pathophysiology, particularly in the field of immune system and host defense. The study of patients carrying mutations in genes encoding for molecules involved in the epigenetic machinery has allowed the identification and better characterization of environment-genome interactions via epigenetics as well as paving the way for the development of new potential therapeutic options. In this review, we summarize current knowledge of the role of epigenetic modifications in the immune system and outline their potential involvement in the pathogenesis of inborn errors of immunity.
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Affiliation(s)
- Roberta Romano
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Francesca Cillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Cristina Moracas
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Chiara Nannola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Elisabetta Toriello
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Antonio De Rosa
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emma Coppola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Nicola Brunetti-Pierri
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Claudio Pignata
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
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14
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Solé P, Santamaria P. Re-Programming Autoreactive T Cells Into T-Regulatory Type 1 Cells for the Treatment of Autoimmunity. Front Immunol 2021; 12:684240. [PMID: 34335585 PMCID: PMC8320845 DOI: 10.3389/fimmu.2021.684240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
Systemic delivery of peptide-major histocompatibility complex (pMHC) class II-based nanomedicines can re-program cognate autoantigen-experienced CD4+ T cells into disease-suppressing T-regulatory type 1 (TR1)-like cells. In turn, these TR1-like cells trigger the formation of complex regulatory cell networks that can effectively suppress organ-specific autoimmunity without impairing normal immunity. In this review, we summarize our current understanding of the transcriptional, phenotypic and functional make up of TR1-like cells as described in the literature. The true identity and direct precursors of these cells remain unclear, in particular whether TR1-like cells comprise a single terminally-differentiated lymphocyte population with distinct transcriptional and epigenetic features, or a collection of phenotypically different subsets sharing key regulatory properties. We propose that detailed transcriptional and epigenetic characterization of homogeneous pools of TR1-like cells will unravel this conundrum.
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Affiliation(s)
- Patricia Solé
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Pere Santamaria
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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15
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Abstract
T lymphocytes undergo carefully orchestrated programming during development in the thymus and subsequently during differentiation in the periphery. This intricate specification allows for cell-type and context-specific transcriptional programs that regulate immune responses to infection and malignancy. Epigenetic changes, including histone modifications and covalent modification of DNA itself through DNA methylation, are now recognized to play a critical role in these cell-fate decisions. DNA methylation is mediated primarily by the actions of the DNA methyltransferase (DNMT) and ten-eleven-translocation (TET) families of epigenetic enzymes. In this review, we discuss the role of DNA methylation and its enzymatic regulators in directing the development and differentiation of CD4+ and CD8+ T-cells.
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Affiliation(s)
- Luis O Correa
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI
| | - Martha S Jordan
- Department of Pathology and Laboratory Medicine; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shannon A Carty
- Department of Internal Medicine, Division of Hematology and Oncology; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
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16
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Shao K, Pu W, Zhang J, Guo S, Qian F, Glurich I, Jin Q, Ma Y, Ju S, Zhang Z, Ding W. DNA hypermethylation contributes to colorectal cancer metastasis by regulating the binding of CEBPB and TFCP2 to the CPEB1 promoter. Clin Epigenetics 2021; 13:89. [PMID: 33892791 PMCID: PMC8063327 DOI: 10.1186/s13148-021-01071-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/07/2021] [Indexed: 01/05/2023] Open
Abstract
Background Aberrant DNA methylation has been firmly established as a factor contributing to the pathogenesis of colorectal cancer (CRC) via its capacity to silence tumour suppressor genes. However, the methylation status of multiple tumour suppressor genes and their roles in promoting CRC metastasis are not well characterised. Methods We explored the methylation and expression profiles of CPEB1 (the gene encoding cytoplasmic polyadenylation element-binding protein 1), a candidate CRC tumour suppressor gene, using The Cancer Genome Atlas (TCGA) database and validated these results in both CRC cell lines and cells from Han Chinese CRC patients (n = 104). The functional role of CPEB1 in CRC was examined in experiments performed in vitro and in vivo. A candidate transcription factor capable of regulating CPEB1 expression was predicted in silico and validated by luciferase reporter, DNA pull-down, and electrophoretic mobility shift assays. Results Hypermethylation and decreased expression of CPEB1 in CRC tumour tissues were revealed by TCGA database. We also identified a significant inverse correlation (Pearson’s R = − 0.43, P < 0.001) between promoter methylation and CPEB1 expression. We validated these results in CRC samples and two CRC cell lines. We also demonstrated that up-regulation of CPEB1 resulted in significantly decreased tumour growth, migration, invasion, and tumorigenicity and promoted tumour cell apoptosis both in vitro and in vivo. We identified the transcription factors CCAAT enhancer-binding protein beta (CEBPB) and transcription factor CP2 (TFCP2) as critical regulators of CPEB1 expression. Hypermethylation of the CPEB1 promoter resulted in a simultaneous increase in the capacity for TFCP2 binding and a decreased likelihood of CEBPB binding, both of which led to diminished expression of CPEB1. Conclusions Our results identified a novel tumour-suppressive role of CPEB1 in CRC and found that hypermethylation of the CPEB1 promoter may lead to diminished expression due to decreased chromatin accessibility and transcription factor binding. Collectively, these results suggest a potential role for CPEB1 in the diagnosis and treatment of CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01071-z.
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Affiliation(s)
- Keke Shao
- Department of Laboratory Medicine, the First People's Hospital of Yancheng City/Affiliated Hospital 4 of Nantong University, Yancheng, Jiangsu Province, China
| | - Weilin Pu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianfeng Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Fei Qian
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Ingrid Glurich
- Office of Research Support Services, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Qing Jin
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Yanyun Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Six Industrial Research Institute, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Weifeng Ding
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China.
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17
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Chu JM, Pease NA, Kueh HY. In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation. Immunol Rev 2021; 300:134-151. [PMID: 33734444 PMCID: PMC8005465 DOI: 10.1111/imr.12946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022]
Abstract
Proper timing of gene expression is central to lymphocyte development and differentiation. Lymphocytes often delay gene activation for hours to days after the onset of signaling components, which act on the order of seconds to minutes. Such delays play a prominent role during the intricate choreography of developmental events and during the execution of an effector response. Though a number of mechanisms are sufficient to explain timing at short timescales, it is not known how timing delays are implemented over long timescales that may span several cell generations. Based on the literature, we propose that a class of cis-regulatory elements, termed "timing enhancers," may explain how timing delays are controlled over these long timescales. By considering chromatin as a kinetic barrier to state switching, the timing enhancer model explains experimentally observed dynamics of gene expression where other models fall short. In this review, we elaborate on features of the timing enhancer model and discuss the evidence for its generality throughout development and differentiation. We then discuss potential molecular mechanisms underlying timing enhancer function. Finally, we explore recent evidence drawing connections between timing enhancers and genetic risk for immunopathology. We argue that the timing enhancer model is a useful framework for understanding how cis-regulatory elements control the central dimension of timing in lymphocyte biology.
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Affiliation(s)
- Jonathan M Chu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
| | - Nicholas A Pease
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
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18
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Frias AB, Boi SK, Lan X, Youngblood B. Epigenetic regulation of T cell adaptive immunity. Immunol Rev 2021; 300:9-21. [PMID: 33644866 DOI: 10.1111/imr.12943] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022]
Abstract
The conceptualization of adaptive immunity, founded on the observation of immunological memory, has served as the basis for modern vaccination and immunotherapy approaches. This fundamental concept has allowed immunologists to explore mechanisms that enable humoral and cellular lymphocytes to tailor immune response functions to a wide array of environmental insults and remain poised for future pathogenic encounters. Until recently, for T cells it has remained unclear how memory differentiation acquires and sustains a gene expression program that grants a cell with a capacity for a heightened recall response. Recent investigations into this critical question have identified epigenetic programs as a causal molecular mechanism governing T cell subset specification and immunological memory. Here, we outline the studies that have illustrated this concept and posit on how insights into T cell adaptive immunity can be applied to improve upon existing immunotherapies.
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Affiliation(s)
- Adolfo B Frias
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shannon K Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Lan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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19
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Loss of MBD2 affects early T cell development by inhibiting the WNT signaling pathway. Exp Cell Res 2020; 398:112400. [PMID: 33271126 DOI: 10.1016/j.yexcr.2020.112400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 12/30/2022]
Abstract
DNA methylation alters the expression of certain genes without any alteration to the DNA sequence and is a dynamic process during normal hematopoietic differentiation. As an epigenetic regulator, methyl-CpG-binding domain protein 2 (MBD2) is an important member of the MBD protein family and is acknowledged as a "reader" of DNA methylation. We used a mouse model to study the effects of MBD2 on the early development of T cells. Here, we found that MBD2 deficiency led to retardation of T cell differentiation at the DN3 stage. Meanwhile, decreased proliferative capacity and increased apoptosis were detected in Mbd2-/- DN thymocytes. Furthermore, we found the WNT pathway was significantly down-regulated in Mbd2-/- DN thymocytes: DKK1 (Dickkopf-1) expression was significantly increased, while TCF7 (transcription factor 7) and c-MYC were down-regulated. Thus, these findings established that MBD2 acted as a dominant regulator to imprint DN T cell development via the WNT pathway.
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20
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Guirguis AA, Liddicoat BJ, Dawson MA. The old and the new: DNA and RNA methylation in normal and malignant hematopoiesis. Exp Hematol 2020; 90:1-11. [PMID: 32961299 DOI: 10.1016/j.exphem.2020.09.193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022]
Abstract
Whilst DNA cytosine methylation is the oldest and most well-studied epigenetic modification, basking in its glory days, it may be soon overshadowed by the new kid on the block: RNA adenosine methylation. This juxtaposition is indeed superficial, and a deep exploration toward the fundamental requirements for these essential epigenetic marks provides a clear perspective on their converging and synergistic roles. The recent discovery that both of these modifications are essential for preventing inappropriate activation of the intracellular innate immune responses to endogenous transcripts has provided a lot of interest in targeting them therapeutically as a means to improve cancer immunogenicity. Here we discuss the potential physiological function for DNA and RNA methylation in normal hematopoiesis and how these pervasive epigenetic marks are exploited in cancer, and provide suggestions for future research with a focus on leveraging this knowledge to uncover novel therapeutic targets.
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Affiliation(s)
- Andrew A Guirguis
- Peter MacCallum Cancer Centre, Melbourne Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.
| | - Brian J Liddicoat
- Peter MacCallum Cancer Centre, Melbourne Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia; Centre for Cancer Research, University of Melbourne, Melbourne, Australia.
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21
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Mudd JC, Lai S, Shah S, Rahmberg A, Flynn JK, Starke CE, Perkins MR, Ransier A, Darko S, Douek DC, Hirsch VM, Cameron M, Brenchley JM. Epigenetic silencing of CD4 expression in nonpathogenic SIV infection in African green monkeys. JCI Insight 2020; 5:139043. [PMID: 32841214 PMCID: PMC7526541 DOI: 10.1172/jci.insight.139043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/13/2020] [Indexed: 01/19/2023] Open
Abstract
African green monkeys (AGMs) are natural hosts of SIV that postthymically downregulate CD4 to maintain a large population of CD4-CD8aa+ virus-resistant cells with Th functionality, which can result in AGMs becoming apparently cured of SIVagm infection. To understand the mechanisms of this process, we performed genome-wide transcriptional analysis on T cells induced to downregulate CD4 in vitro from AGMs and closely related patas monkeys and T cells that maintain CD4 expression from rhesus macaques. In T cells that downregulated CD4, pathway analysis revealed an atypical regulation of the DNA methylation machinery, which was reversible when pharmacologically targeted with 5-aza-2 deoxycytidine. This signature was driven largely by the dioxygenase TET3, which became downregulated with loss of CD4 expression. CpG motifs within the AGM CD4 promoter region became methylated during CD4 downregulation in vitro and were stably imprinted in AGM CD4-CD8aa+ T cells sorted directly ex vivo. These results suggest that AGMs use epigenetic mechanisms to durably silence the CD4 gene. Manipulation of these mechanisms could provide avenues for modulating SIV and HIV-1 entry receptor expression in hosts that become progressively infected with SIV, which could lead to novel therapeutic interventions aimed to reduce HIV viremia in vivo.
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Affiliation(s)
- Joseph C Mudd
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
| | - Stephen Lai
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
| | - Sanjana Shah
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
| | - Andrew Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
| | - Jacob K Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
| | - Carly E Starke
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
| | - Molly R Perkins
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
| | - Amy Ransier
- Human Immunology Section, Vaccine Research Center, and
| | - Sam Darko
- Human Immunology Section, Vaccine Research Center, and
| | | | - Vanessa M Hirsch
- Nonhuman Primate Virology Section, Laboratory of Molecular Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Mark Cameron
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research
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22
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Zhang SC, Wang MY, Feng JR, Chang Y, Ji SR, Wu Y. Reversible promoter methylation determines fluctuating expression of acute phase proteins. eLife 2020; 9:51317. [PMID: 32223889 PMCID: PMC7136028 DOI: 10.7554/elife.51317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 03/27/2020] [Indexed: 12/15/2022] Open
Abstract
Acute phase reactants (APRs) are secretory proteins exhibiting large expression changes in response to proinflammatory cytokines. Here we show that the expression pattern of a major human APR, that is C-reactive protein (CRP), is casually determined by DNMT3A and TET2-tuned promoter methylation status. CRP features a CpG-poor promoter with its CpG motifs located in binding sites of STAT3, C/EBP-β and NF-κB. These motifs are highly methylated at the resting state, but undergo STAT3- and NF-κB-dependent demethylation upon cytokine stimulation, leading to markedly enhanced recruitment of C/EBP-β that boosts CRP expression. Withdrawal of cytokines, by contrast, results in a rapid recovery of promoter methylation and termination of CRP induction. Further analysis suggests that reversible methylation also regulates the expression of highly inducible genes carrying CpG-poor promoters with APRs as representatives. Therefore, these CpG-poor promoters may evolve CpG-containing TF binding sites to harness dynamic methylation for prompt and reversible responses.
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Affiliation(s)
- Shi-Chao Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ming-Yu Wang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jun-Rui Feng
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Yue Chang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shang-Rong Ji
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yi Wu
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
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23
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Seo W, Taniuchi I. The Roles of RUNX Family Proteins in Development of Immune Cells. Mol Cells 2020; 43:107-113. [PMID: 31926543 PMCID: PMC7057832 DOI: 10.14348/molcells.2019.0291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/12/2019] [Indexed: 02/04/2023] Open
Abstract
The Runt-related transcription factors (RUNX) transcription factors have been known for their critical roles in numerous developmental processes and diseases such as autoimmune disorders and cancer. Especially, RUNX proteins are best known for their roles in hematopoiesis, particularly during the development of T cells. As scientists discover more types of new immune cells, the functional diversity of RUNX proteins also has been increased over time. Furthermore, recent research has revealed complicated transcriptional networks involving RUNX proteins by the current technical advances. Databases established by next generation sequencing data analysis has identified ever increasing numbers of potential targets for RUNX proteins and other transcription factors. Here, we summarize diverse functions of RUNX proteins mainly on lymphoid lineage cells by incorporating recent discoveries.
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Affiliation(s)
- Wooseok Seo
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 30-0045, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 30-0045, Japan
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24
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Pace L, Amigorena S. Epigenetics of T cell fate decision. Curr Opin Immunol 2020; 63:43-50. [PMID: 32066083 DOI: 10.1016/j.coi.2020.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
The changes of transcription factor activity and chromatin dynamics guide functional differentiation of T cell subsets, including commitment to short-lived effectors and long-term survival of memory T cells. Understanding the lineage relationships among the different stages of effector and memory differentiation has profound therapeutic implications for the development of new vaccine and immunotherapy protocols. Here we review the contribution of chromatin architecture to T cell specification, focusing on the interplay between epigenetic changes and transcriptional programs linked to T cell plasticity, commitment and memory. We will also discuss the translational implications of epigenetic control in the context of infections and cancer.
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Affiliation(s)
- Luigia Pace
- Armenise-Harvard Immune Regulation Unit, IIGM, FPO-IRCCS Candiolo, Turin, Italy.
| | - Sebastian Amigorena
- Institut Curie, PSL Research University, Paris, France; INSERM U932, France.
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25
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de la Calle-Fabregat C, Morante-Palacios O, Ballestar E. Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease. Genes (Basel) 2020; 11:E110. [PMID: 31963661 PMCID: PMC7017047 DOI: 10.3390/genes11010110] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Immune cells are one of the most complex and diverse systems in the human organism. Such diversity implies an intricate network of different cell types and interactions that are dependently interconnected. The processes by which different cell types differentiate from progenitors, mature, and finally exert their function requires an orchestrated succession of molecular processes that determine cell phenotype and function. The acquisition of these phenotypes is highly dependent on the establishment of unique epigenetic profiles that confer identity and function on the various types of effector cells. These epigenetic mechanisms integrate microenvironmental cues into the genome to establish specific transcriptional programs. Epigenetic modifications bridge environment and genome regulation and play a role in human diseases by their ability to modulate physiological programs through external stimuli. DNA methylation is one of the most ubiquitous, stable, and widely studied epigenetic modifications. Recent technological advances have facilitated the generation of a vast amount of genome-wide DNA methylation data, providing profound insights into the roles of DNA methylation in health and disease. This review considers the relevance of DNA methylation to immune system cellular development and function, as well as the participation of DNA methylation defects in immune-mediated pathologies, illustrated by selected paradigmatic diseases.
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Affiliation(s)
| | | | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; (C.d.l.C.-F.); (O.M.-P.)
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26
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Hiam D, Simar D, Laker R, Altıntaş A, Gibson-Helm M, Fletcher E, Moreno-Asso A, Trewin AJ, Barres R, Stepto NK. Epigenetic Reprogramming of Immune Cells in Women With PCOS Impact Genes Controlling Reproductive Function. J Clin Endocrinol Metab 2019; 104:6155-6170. [PMID: 31390009 DOI: 10.1210/jc.2019-01015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) is a chronic disease affecting reproductive function and whole-body metabolism. Although the etiology is unclear, emerging evidence indicates that the epigenetics may be a contributing factor. OBJECTIVE To determine the role of global and genome-wide epigenetic modifications in specific immune cells in PCOS compared with controls and whether these could be related to clinical features of PCOS. DESIGN Cross-sectional study. PARTICIPANTS Women with (n = 17) or without PCOS (n = 17). SETTING Recruited from the general community. MAIN OUTCOME MEASURES Isolated peripheral blood mononuclear cells were analyzed using multicolor flow cytometry methods to determine global DNA methylation levels in a cell-specific fashion. Transcriptomic and genome-wide DNA methylation analyses were performed on T helper cells using RNA sequencing and reduced representation bisulfite sequencing. RESULTS Women with PCOS had lower global DNA methylation in monocytes (P = 0.006) and in T helper (P = 0.004), T cytotoxic (P = 0.004), and B cells (P = 0.03). Specific genome-wide DNA methylation analysis of T helper cells from women with PCOS identified 5581 differentially methylated CpG sites. Functional gene ontology enrichment analysis showed that genes located at the proximity of differentially methylated CpG sites belong to pathways related to reproductive function and immune cell function. However, these genes were not altered at the transcriptomic level. CONCLUSIONS It was shown that PCOS is associated with global and gene-specific DNA methylation remodeling in a cell type-specific manner. Further investigation is warranted to determine whether epigenetic reprogramming of immune cells is important in determining the different phenotypes of PCOS.
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Affiliation(s)
- Danielle Hiam
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - David Simar
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Rhianna Laker
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ali Altıntaş
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Melanie Gibson-Helm
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Elly Fletcher
- Baker Heart and Disease Institute, Melbourne, Victoria, Australia
| | - Alba Moreno-Asso
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Adam J Trewin
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Romain Barres
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Nigel K Stepto
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Medicine-Western Health, School of Medicine, Faculty of Medicine, Dentistry, and Health Science, Melbourne, Australia
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27
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Ibáñez-Cabellos JS, Seco-Cervera M, Osca-Verdegal R, Pallardó FV, García-Giménez JL. Epigenetic Regulation in the Pathogenesis of Sjögren Syndrome and Rheumatoid Arthritis. Front Genet 2019; 10:1104. [PMID: 31798626 PMCID: PMC6863924 DOI: 10.3389/fgene.2019.01104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/11/2019] [Indexed: 01/01/2023] Open
Abstract
Autoimmune rheumatic diseases, such as Sjögren syndrome (SS) and rheumatoid arthritis (RA), are characterized by chronic inflammation and autoimmunity, which cause joint tissue damage and destruction by triggering reduced mobility and debilitation in patients with these diseases. Initiation and maintenance of chronic inflammatory stages account for several mechanisms that involve immune cells as key players and the interaction of the immune cells with other tissues. Indeed, the overlapping of certain clinical and serologic manifestations between SS and RA may indicate that numerous immunologic-related mechanisms are involved in the physiopathology of both these diseases. It is widely accepted that epigenetic pathways play an essential role in the development and function of the immune system. Although many published studies have attempted to elucidate the relation between epigenetic modifications (e.g. DNA methylation, histone post-translational modifications, miRNAs) and autoimmune disorders, the contribution of epigenetic regulation to the pathogenesis of SS and RA is at present poorly understood. This review attempts to shed light from a critical point of view on the identification of the most relevant epigenetic mechanisms related to RA and SS by explaining intricate regulatory processes and phenotypic features of both autoimmune diseases. Moreover, we point out some epigenetic markers which can be used to monitor the inflammation status and the dysregulated immunity in SS and RA. Finally, we discuss the inconvenience of using epigenetic data obtained from bulk immune cell populations instead specific immune cell subpopulations.
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Affiliation(s)
- José Santiago Ibáñez-Cabellos
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Marta Seco-Cervera
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Rebeca Osca-Verdegal
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
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28
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Abstract
During thymocyte development at the double positive stage, thymocytes are subjected to a TCR quality check process termed "thymocyte selection." TCRs with proper binding capabilities to MHC molecules (with self-peptide) are able to transduce cell survival signals and allow the continuing of development to single positive T cells. It has been known that TCRs in DP cells can transduce signals with higher efficiency than peripheral mature T cells, even though they share most of the signaling components. Recent studies have revealed some thymocyte-specific signaling modulators including Themis and Tespa1. The activation of TCR signaling during positive selection results in the activation of several key transcription factors and extensive gene expression change, which has been revealed by newly developed systemic transcriptome analysis tools, and could be used for the evaluation of positive selection process. The fate determination postpositive selection is also governed on the epigenetic level including both DNA methylation and histone modifications.
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Affiliation(s)
- Jun Lyu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Lie Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Linrong Lu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China; Department of Dermatology and Rheumatology in Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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29
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Karagianni P, Tzioufas AG. Epigenetic perspectives on systemic autoimmune disease. J Autoimmun 2019; 104:102315. [PMID: 31421964 DOI: 10.1016/j.jaut.2019.102315] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/28/2019] [Indexed: 12/12/2022]
Abstract
Autoimmune diseases are characterized by increased reactivity of the immune system towards self-antigens, causing tissue damage. Although their etiology remains largely unknown, genetic, microbial, environmental and psychological factors are recognized as contributing elements. Epigenetic changes, including covalent modifications of the DNA and histones, are critical signaling mediators between the genome and the environment, and thus potent regulators of cellular functions. The most extensively studied epigenetic modifications are Cytosine DNA methylation and histone acetylation and methylation on various residues. These are thought to affect chromatin structure and binding of specific effectors that regulate transcription, replication, and other processes. Recent studies have uncovered significant epigenetic alterations in cells or tissues derived from autoimmune disease patients compared to samples from healthy individuals and have linked them with disease phenotypes. Epigenetic changes in specific genes correlate with upregulated or downregulated transcription. For instance, in many systems, reduced DNA methylation and increased histone acetylation of interferon-inducible genes correlate with their increased expression in autoimmune disease patients. Also, reduced DNA methylation of retroelements has been proposed as an activating mechanism and has been linked with increased immune reactivity, while epigenetic differences on the X chromosome could indicate incomplete dosage compensation and explain to some extent the increased susceptibility of females over males towards the development of most autoimmune diseases. Besides changes in epigenetic modifications, differences in the levels of many enzymes catalyzing the addition or removal of these marks as well as proteins that recognize them and function as effector molecules have also been detected in autoimmune patients. Although the existing knowledge cannot fully explain whether epigenetic alterations cause or follow the increased immune activation, their characterization is very useful for understanding the pathogenetic mechanisms and complements genetic and clinical studies. Furthermore, specific epigenetic marks have the potential to serve as biomarkers for disease status, prognosis, and response to treatment. Finally, epigenetic factors are currently being examined as candidate therapeutic targets.
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Affiliation(s)
- Panagiota Karagianni
- Department of Pathophysiology, School of Medicine, University of Athens, Mikras Asias Str 75, 115 27, Athens, Greece
| | - Athanasios G Tzioufas
- Department of Pathophysiology, School of Medicine, University of Athens, Mikras Asias Str 75, 115 27, Athens, Greece.
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30
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Abstract
A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4+ helper and CD8+ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively. Together with increasing knowledge of epigenetic regulators, these findings have advanced our understanding of the transcription factor network regulating the CD4/CD8 dichotomy. It has also become apparent that CD4+ T cells retain developmental plasticity, allowing them to acquire cytotoxic activity in the periphery. Despite such advances, further studies are necessary to identify the molecular links between TCR signaling and the nuclear machinery regulating expression of ThPOK and Runx3.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan;
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31
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Zeidan N, Damen H, Roy DC, Dave VP. Critical Role for TCR Signal Strength and MHC Specificity in ThPOK-Induced CD4 Helper Lineage Choice. THE JOURNAL OF IMMUNOLOGY 2019; 202:3211-3225. [PMID: 31036767 DOI: 10.4049/jimmunol.1801464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023]
Abstract
Sustained TCR signaling is critical for ThPOK induction in MHC class II (MHCII)-signaled thymocytes leading to the CD4 helper lineage commitment. ThPOK suppresses the cytotoxic program in the signaled thymocytes and is shown to be necessary and sufficient for the CD4 helper lineage choice. Accordingly, loss and gain of ThPOK function redirects MHCII- and MHC class I (MHCI)-signaled thymocytes into the CD8 cytotoxic and CD4 helper lineage, respectively. However, the impact of a defined ThPOK level on the CD4 helper lineage choice of MHCII- and MHCI-specific thymocytes and the role of TCR signaling in this process is not evaluated. Equally, it is not clear if suppression of the cytotoxic program by ThPOK is sufficient in redirecting MHCI-restricted thymocytes into the CD4 helper lineage. In this study, we have investigated CD8 to CD4 helper lineage redirection in three independent ThPOK overexpressing transgenic mouse lines. Our analysis shows that one of the transgenic lines, despite overexpressing ThPOK compared with wild-type CD4 mature T cells and compromising cytotoxic program, failed to redirect all MHCI-signaled thymocytes into the CD4 helper lineage, resulting in the continued presence of CD8+ mature T cells and the generation of a large number of double negative mature T cells. Critically, the same ThPOK transgene completely restored the CD4 helper lineage commitment of MHCII-specific Thpok -/- thymocytes. Importantly, augmenting TCR signaling significantly enhanced the ThPOK-mediated CD4 helper lineage choice of MHCI-specific thymocytes but was still substantially less efficient than that of MHCII-specific thymocytes expressing the same amount of ThPOK. Together, these data suggest that the ThPOK-induced CD4 helper lineage commitment is strongly influenced by TCR signal strength and MHC specificity of developing thymocytes.
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Affiliation(s)
- Nabil Zeidan
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada; and
| | - Hassan Damen
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada
| | - Denis-Claude Roy
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Vibhuti P Dave
- Département d'Immunologie-Oncologie, Centre de Recherche Hôpital Maisonneuve-Rosemont, Montreal, Quebec H1T 2M4, Canada; .,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada; and
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32
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Ng C, Aichinger M, Nguyen T, Au C, Najar T, Wu L, Mesa KR, Liao W, Quivy JP, Hubert B, Almouzni G, Zuber J, Littman DR. The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells. Genes Dev 2019; 33:669-683. [PMID: 30975723 PMCID: PMC6546056 DOI: 10.1101/gad.322024.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/22/2019] [Indexed: 12/12/2022]
Abstract
In this study, Ng et al. investigated the maintenance of silent gene states and how the Cd4 gene is stably repressed in CD8+ T cells. Using CRISPR and shRNA screening, they identified the histone chaperone CAF-1 as a critical component for Cd4 repression and propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone-modifying enzymes. The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the Cd4 gene is stably repressed in CD8+ T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for Cd4 repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1/2 and the histone demethylase LSD1, enzymes that also participate in Cd4 silencing. When CAF-1 was lacking, Cd4 derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the Cd4 locus. Instead, Dnmt3a deficiency sensitized CD8+ T cells to Cd4 derepression mediated by compromised functions of histone-modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone-modifying enzymes.
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Affiliation(s)
- Charles Ng
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Martin Aichinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Tung Nguyen
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Christy Au
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Tariq Najar
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Lin Wu
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Kai R Mesa
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Will Liao
- New York Genome Center, New York, New York 10013, USA
| | - Jean-Pierre Quivy
- UMR3664, Centre National de la Recherche Scientifique, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, PSL Research University, F-75005 Paris, France
| | | | - Genevieve Almouzni
- UMR3664, Centre National de la Recherche Scientifique, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, New York, New York 10016, USA
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33
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Bosselut R. Control of Intra-Thymic αβ T Cell Selection and Maturation by H3K27 Methylation and Demethylation. Front Immunol 2019; 10:688. [PMID: 31001282 PMCID: PMC6456692 DOI: 10.3389/fimmu.2019.00688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022] Open
Abstract
In addition to transcription factor binding, the dynamics of DNA modifications (methylation) and chromatin structure are essential contributors to the control of transcription in eukaryotes. Research in the past few years has emphasized the importance of histone H3 methylation at lysine 27 for lineage specific gene repression, demonstrated that deposition of this mark at specific genes is subject to differentiation-induced changes during development, and identified enzymatic activities, methyl transferases and demethylases, that control these changes. The present review discusses the importance of these mechanisms during intrathymic αβ T cell selection and late differentiation.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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Sinclair LV, Howden AJM, Brenes A, Spinelli L, Hukelmann JL, Macintyre AN, Liu X, Thomson S, Taylor PM, Rathmell JC, Locasale JW, Lamond AI, Cantrell DA. Antigen receptor control of methionine metabolism in T cells. eLife 2019; 8:e44210. [PMID: 30916644 PMCID: PMC6497464 DOI: 10.7554/elife.44210] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
Immune activated T lymphocytes modulate the activity of key metabolic pathways to support the transcriptional reprograming and reshaping of cell proteomes that permits effector T cell differentiation. The present study uses high resolution mass spectrometry and metabolic labelling to explore how murine T cells control the methionine cycle to produce methyl donors for protein and nucleotide methylations. We show that antigen receptor engagement controls flux through the methionine cycle and RNA and histone methylations. We establish that the main rate limiting step for protein synthesis and the methionine cycle is control of methionine transporter expression. Only T cells that respond to antigen to upregulate and sustain methionine transport are supplied with methyl donors that permit the dynamic nucleotide methylations and epigenetic reprogramming that drives T cell differentiation. These data highlight how the regulation of methionine transport licenses use of methionine for multiple fundamental processes that drive T lymphocyte proliferation and differentiation.
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Affiliation(s)
- Linda V Sinclair
- Cell Signalling and ImmunologyUniversity of DundeeDundeeUnited Kingdom
| | - Andrew JM Howden
- Cell Signalling and ImmunologyUniversity of DundeeDundeeUnited Kingdom
| | - Alejandro Brenes
- Centre for Gene Regulation and ExpressionUniversity of DundeeDundeeUnited Kingdom
| | - Laura Spinelli
- Cell Signalling and ImmunologyUniversity of DundeeDundeeUnited Kingdom
| | - Jens L Hukelmann
- Centre for Gene Regulation and ExpressionUniversity of DundeeDundeeUnited Kingdom
| | | | - Xiaojing Liu
- Pharmacology and Cancer BiologyDuke UniversityDurhamUnited States
| | - Sarah Thomson
- Cell Signalling and ImmunologyUniversity of DundeeDundeeUnited Kingdom
| | - Peter M Taylor
- Cell Signalling and ImmunologyUniversity of DundeeDundeeUnited Kingdom
| | - Jeffrey C Rathmell
- Center for ImmunobiologyVanderbilt University Medical CenterNashvilleUnited States
| | - Jason W Locasale
- Pharmacology and Cancer BiologyDuke UniversityDurhamUnited States
| | - Angus I Lamond
- Centre for Gene Regulation and ExpressionUniversity of DundeeDundeeUnited Kingdom
| | - Doreen A Cantrell
- Cell Signalling and ImmunologyUniversity of DundeeDundeeUnited Kingdom
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Ntranos A, Ntranos V, Bonnefil V, Liu J, Kim-Schulze S, He Y, Zhu Y, Brandstadter R, Watson CT, Sharp AJ, Katz Sand I, Casaccia P. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain 2019; 142:647-661. [PMID: 30698680 PMCID: PMC6821213 DOI: 10.1093/brain/awy344] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023] Open
Abstract
Cell-permeable formulations of metabolites, such as fumaric acid esters, have been used as highly effective immunomodulators in patients with multiple sclerosis and yet their mechanism of action remains elusive. Since fumaric acid esters are metabolites, and cell metabolism is highly intertwined with the epigenetic regulation of gene expression, we investigated whether this metabolic-epigenetic interplay could be leveraged for therapeutic purposes. To this end we recruited 47 treatment-naïve and 35 fumaric acid ester-treated patients with multiple sclerosis, as well as 16 glatiramer acetate-treated patients as a non-metabolite treatment control. Here we identify a significant immunomodulatory effect of fumaric acid esters on the expression of the brain-homing chemokine receptor CCR6 in CD4 and CD8 T cells of patients with multiple sclerosis, which include T helper-17 and T cytotoxic-17 cells. We report differences in DNA methylation of CD4 T cells isolated from untreated and treated patients with multiple sclerosis, using the Illumina EPIC 850K BeadChip. We first demonstrate that Krebs cycle intermediates, such as fumaric acid esters, have a significantly higher impact on epigenome-wide DNA methylation changes in CD4 T cells compared to amino-acid polymers such as glatiramer acetate. We then define a fumaric acid ester treatment-specific hypermethylation effect on microRNA MIR-21, which is critical for the differentiation of T helper-17 cells. This hypermethylation effect was attributed to the subpopulation of T helper-17 cells using a decomposition analysis and was further validated in an independent prospective cohort of seven patients before and after treatment with fumaric acid esters. In vitro treatment of CD4 and CD8 T cells with fumaric acid esters supported a direct and dose-dependent effect on DNA methylation at the MIR-21 promoter. Finally, the upregulation of miR-21 transcripts and CCR6 expression was inhibited if CD4 or CD8 T cells stimulated under T helper-17 or T cytotoxic-17 polarizing conditions were treated with fumaric acid esters in vitro. These data collectively define a direct link between fumaric acid ester treatment and hypermethylation of the MIR-21 locus in both CD4 and CD8 T cells and suggest that the immunomodulatory effect of fumaric acid esters in multiple sclerosis is at least in part due to the epigenetic regulation of the brain-homing CCR6+ CD4 and CD8 T cells.
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Affiliation(s)
- Achilles Ntranos
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Valentina Bonnefil
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
| | - Jia Liu
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ye He
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
| | - Yunjiao Zhu
- Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Brandstadter
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Corey T Watson
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Andrew J Sharp
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilana Katz Sand
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrizia Casaccia
- Neuroscience, Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA
- Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Morales-Nebreda L, McLafferty FS, Singer BD. DNA methylation as a transcriptional regulator of the immune system. Transl Res 2019; 204:1-18. [PMID: 30170004 PMCID: PMC6331288 DOI: 10.1016/j.trsl.2018.08.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022]
Abstract
DNA methylation is a dynamic epigenetic modification with a prominent role in determining mammalian cell development, lineage identity, and transcriptional regulation. Primarily linked to gene silencing, novel technologies have expanded the ability to measure DNA methylation on a genome-wide scale and uncover context-dependent regulatory roles. The immune system is a prototypic model for studying how DNA methylation patterning modulates cell type- and stimulus-specific transcriptional programs. Preservation of host defense and organ homeostasis depends on fine-tuned epigenetic mechanisms controlling myeloid and lymphoid cell differentiation and function, which shape innate and adaptive immune responses. Dysregulation of these processes can lead to human immune system pathology as seen in blood malignancies, infections, and autoimmune diseases. Identification of distinct epigenotypes linked to pathogenesis carries the potential to validate therapeutic targets in disease prevention and management.
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Affiliation(s)
- Luisa Morales-Nebreda
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Fred S McLafferty
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Benjamin D Singer
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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37
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Yoon BH, Kim M, Kim MH, Kim HJ, Kim JH, Kim JH, Kim J, Kim YS, Lee D, Kang SJ, Kim SY. Dynamic Transcriptome, DNA Methylome, and DNA Hydroxymethylome Networks During T-Cell Lineage Commitment. Mol Cells 2018; 41:953-963. [PMID: 30396239 PMCID: PMC6277565 DOI: 10.14348/molcells.2018.0213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/14/2018] [Accepted: 10/18/2018] [Indexed: 12/27/2022] Open
Abstract
The stepwise development of T cells from a multipotent precursor is guided by diverse mechanisms, including interactions among lineage-specific transcription factors (TFs) and epigenetic changes, such as DNA methylation and hydroxymethylation, which play crucial roles in mammalian development and lineage commitment. To elucidate the transcriptional networks and epigenetic mechanisms underlying T-cell lineage commitment, we investigated genome-wide changes in gene expression, DNA methylation and hydroxymethylation among populations representing five successive stages of T-cell development (DN3, DN4, DP, CD4+, and CD8+) by performing RNA-seq, MBD-seq and hMeDIP-seq, respectively. The most significant changes in the transcriptomes and epigenomes occurred during the DN4 to DP transition. During the DP stage, many genes involved in chromatin modification were up-regulated and exhibited dramatic changes in DNA hydroxymethylation. We also observed 436 alternative splicing events, and approximately 57% (252) of these events occurred during the DP stage. Many stage-specific, differentially methylated regions were observed near the stage-specific, differentially expressed genes. The dynamic changes in DNA methylation and hydroxymethylation were associated with the recruitment of stage-specific TFs. We elucidated interactive networks comprising TFs, chromatin modifiers, and DNA methylation and hope that this study provides a framework for the understanding of the molecular networks underlying T-cell lineage commitment.
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Affiliation(s)
- Byoung-Ha Yoon
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon,
Korea
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
| | - Mirang Kim
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon,
Korea
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
| | - Min-Hyeok Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon,
Korea
| | - Hee-Jin Kim
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
| | - Jeong-Hwan Kim
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
| | - Jong Hwan Kim
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon,
Korea
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
| | - Jina Kim
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon,
Korea
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
| | - Yong Sung Kim
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon,
Korea
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon,
Korea
| | - Suk-Jo Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon,
Korea
| | - Seon-Young Kim
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon,
Korea
- Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,
Korea
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38
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Runx-dependent and silencer-independent repression of a maturation enhancer in the Cd4 gene. Nat Commun 2018; 9:3593. [PMID: 30185787 PMCID: PMC6125603 DOI: 10.1038/s41467-018-05803-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023] Open
Abstract
An intronic silencer, S4, in the Cd4 gene has been shown to be responsible for the helper-lineage-specific expression of CD4; S4 requires Runx complex binding to exert its silencer function against the enhancer-mediated Cd4 activation by modulating the epigenetic state of the Cd4 gene. Here we identify a late-acting maturation enhancer. Bcl11b plays essential roles for activation of both the early-acting proximal enhancer and maturation enhancer of Cd4. Notably, Runx complexes suppress these enhancers by distinct mechanisms. Whereas repression of the proximal enhancer depends on the S4 silencer, the maturation enhancer is repressed by Runx in the absence of S4. Moreover, ThPOK, known to antagonize S4-mediated Cd4 repression, assists Runx complexes to restrain maturation enhancer activation. Distinct modes of S4 silencer action upon distinct enhancers thus unravel a pathway that restricts CD4 expression to helper-lineage cells by silencer-independent and Runx-dependent repression of maturation enhancer activity in cytotoxic-lineage cells. The commitment of helper and cytotoxic lineages for CD4 and CD8 T cells, respectively, is associated with the regulation of Cd4 gene expression. Here the authors show that an intronic silencer, S4, has differential effects and synergy with the RUNX complex to act on two enhancer elements of the CD4 gene to control T cell lineage commitment in the thymus.
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Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development. Nat Commun 2018; 9:3594. [PMID: 30185805 PMCID: PMC6125341 DOI: 10.1038/s41467-018-05834-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/27/2018] [Indexed: 11/30/2022] Open
Abstract
The inheritance of gene expression patterns is dependent on epigenetic regulation, but the establishment and maintenance of epigenetic landscapes during T cell differentiation are incompletely understood. Here we show that two stage-specific Cd4 cis-elements, the previously characterized enhancer E4p and a novel enhancer E4m, coordinately promote Cd4 transcription in mature thymic MHC-II-specific T cells, in part through the canonical Wnt pathway. Specifically, E4p licenses E4m to orchestrate DNA demethylation by TET1 and TET3, which in turn poises the Cd4 locus for transcription in peripheral T cells. Cd4 locus demethylation is important for subsequent Cd4 transcription in activated peripheral T cells wherein these cis-elements become dispensable. By contrast, in developing thymocytes the loss of TET1/3 does not affect Cd4 transcription, highlighting an uncoupled event between transcription and epigenetic modifications. Together our findings reveal an important function for thymic cis-elements in governing gene expression in the periphery via a heritable epigenetic mechanism. The expression of CD4, a critical co-receptor providing T cell help in adaptive immunity, is finely tuned during development. Here the authors show that two enhancer elements, E4p and the newly-defined E4m, coordinate the expression and heritable demethylation of Cd4 in thymocytes but are dispensable for its sustained expression in peripheral T cells.
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40
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Arama C, Quin JE, Kouriba B, Östlund Farrants AK, Troye-Blomberg M, Doumbo OK. Epigenetics and Malaria Susceptibility/Protection: A Missing Piece of the Puzzle. Front Immunol 2018; 9:1733. [PMID: 30158923 PMCID: PMC6104485 DOI: 10.3389/fimmu.2018.01733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022] Open
Abstract
A better understanding of stable changes in regulation of gene expression that result from epigenetic events is of great relevance in the development of strategies to prevent and treat infectious diseases. Histone modification and DNA methylation are key epigenetic mechanisms that can be regarded as marks, which ensure an accurate transmission of the chromatin states and gene expression profiles over generations of cells. There is an increasing list of these modifications, and the complexity of their action is just beginning to be understood. It is clear that the epigenetic landscape plays a fundamental role in most biological processes that involve the manipulation and expression of DNA. Although the molecular mechanism of gene regulation is relatively well understood, the hierarchical order of events and dependencies that lead to protection against infection remain largely unknown. In this review, we propose that host epigenetics is an essential, though relatively under studied, factor in the protection or susceptibility to malaria.
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Affiliation(s)
- Charles Arama
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Jaclyn E Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bourèma Kouriba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | | | - Marita Troye-Blomberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
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41
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Anastasiadi D, Esteve-Codina A, Piferrer F. Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. Epigenetics Chromatin 2018; 11:37. [PMID: 29958539 PMCID: PMC6025724 DOI: 10.1186/s13072-018-0205-1] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is one of the main epigenetic mechanisms for the regulation of gene expression in eukaryotes. In the standard model, methylation in gene promoters has received the most attention since it is generally associated with transcriptional silencing. Nevertheless, recent studies in human tissues reveal that methylation of the region downstream of the transcription start site is highly informative of gene expression. Also, in some cell types and specific genes it has been found that methylation of the first intron, a gene feature typically rich in enhancers, is linked with gene expression. However, a genome-wide, tissue-independent, systematic comparative analysis of the relationship between DNA methylation in the first intron and gene expression across vertebrates has not been explored yet. RESULTS The most important findings of this study are: (1) using different tissues from a modern fish, we show a clear genome-wide, tissue-independent quasi-linear inverse relationship between DNA methylation of the first intron and gene expression. (2) This relationship is conserved across vertebrates, since it is also present in the genomes of a model pufferfish, a model frog and different human tissues. Among the gene features, tissues and species interrogated, the first intron's negative correlation with the gene expression was most consistent. (3) We identified more tissue-specific differentially methylated regions (tDMRs) in the first intron than in any other gene feature. These tDMRs have positive or negative correlation with gene expression, indicative of distinct mechanisms of tissue-specific regulation. (4) Lastly, we identified CpGs in transcription factor binding motifs, enriched in the first intron, the methylation of which tended to increase with the distance from the first exon-first intron boundary, with a concomitant decrease in gene expression. CONCLUSIONS Our integrative analysis clearly reveals the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies should be focused.
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Affiliation(s)
- Dafni Anastasiadi
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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Barwick BG, Scharer CD, Martinez RJ, Price MJ, Wein AN, Haines RR, Bally APR, Kohlmeier JE, Boss JM. B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation. Nat Commun 2018; 9:1900. [PMID: 29765016 PMCID: PMC5953949 DOI: 10.1038/s41467-018-04234-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/10/2018] [Indexed: 12/22/2022] Open
Abstract
B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cellular division and is linked to DNA hypomethylation. Conversely, little is known about how de novo deposition of DNA methylation affects B cell fate and function. Here we show that genetic deletion of the de novo DNA methyltransferases Dnmt3a and Dnmt3b (Dnmt3-deficient) in mouse B cells results in normal B cell development and maturation, but increased cell activation and expansion of the germinal center B cell and plasma cell populations upon immunization. Gene expression is mostly unaltered in naive and germinal center B cells, but dysregulated in Dnmt3-deficient plasma cells. Differences in gene expression are proximal to Dnmt3-dependent DNA methylation and chromatin changes, both of which coincide with E2A and PU.1-IRF composite-binding motifs. Thus, de novo DNA methylation limits B cell activation, represses the plasma cell chromatin state, and regulates plasma cell differentiation.
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Affiliation(s)
- Benjamin G Barwick
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, 1701 Uppergate Drive, WCI 4060 C, Atlanta, GA, 30322, USA
| | - Christopher D Scharer
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Ryan J Martinez
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
- Department of Medicine, Emory University School of Medicine, 1648 Pierce Dr. NE, Atlanta, GA, 30307, USA
| | - Madeline J Price
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Alexander N Wein
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Robert R Haines
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Alexander P R Bally
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
- Department of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine, 954 Gatewood Rd NE, Suite 3052, Atlanta, GA, 30329, USA
| | - Jacob E Kohlmeier
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA.
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43
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Verbaro DJ, Sakurai N, Kim B, Shinkai Y, Egawa T. Cutting Edge: The Histone Methyltransferase G9a Is Required for Silencing of Helper T Lineage-Associated Genes in Proliferating CD8 T Cells. THE JOURNAL OF IMMUNOLOGY 2018; 200:3891-3896. [PMID: 29720423 DOI: 10.4049/jimmunol.1701700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/11/2018] [Indexed: 11/19/2022]
Abstract
Helper versus cytotoxic T lineage decision in the thymus has been studied as a model for silencing of alternative lineage genes. Although the transcription factor RUNX3 is required for the initiation of Cd4 silencing in developing CD8 T cells, it is unknown how silencing of Cd4 and other helper T lineage genes is maintained. We show that the histone methyltransferase G9a is necessary for silencing helper T lineage genes in proliferating mouse CD8 T cells. Despite normal initial Cd4 downregulation, G9a-deficient CD8 T cells derepress Cd4 and other helper lineage genes during repeated division in lymphopenia or in response to tumor Ag. However, G9a was dispensable for continued silencing of those genes in CD8 T cells that respond to infection by Listeria monocytogenes These results demonstrate that G9a facilitates maintenance of cellular identity of CD8 T cells during cell division, which is further reinforced by inflammatory signals.
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Affiliation(s)
- Daniel J Verbaro
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Nagisa Sakurai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Byungil Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
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Inhibition of Enhancer of zeste homolog 2 (EZH2) induces natural killer cell-mediated eradication of hepatocellular carcinoma cells. Proc Natl Acad Sci U S A 2018; 115:E3509-E3518. [PMID: 29581297 DOI: 10.1073/pnas.1802691115] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural killer (NK) cell-mediated tumor cell eradication could inhibit tumor initiation and progression. However, the factors that regulate NK cell-mediated cancer cell eradication remain unclear. We determined that hepatocellular carcinoma (HCC) cells exhibit transcriptional down-regulation of NK group 2D (NKG2D) ligands and are largely resistant to NK cell-mediated eradication. Because the down-regulation of NKG2D ligands occurred at the transcriptional level, we tested 32 chemical inhibitors of epigenetic regulators for their ability to re-express NKG2D ligands and enhance HCC cell eradication by NK cells and found that Enhancer of zeste homolog 2 (EZH2) was a transcriptional repressor of NKG2D ligands. The inhibition of EZH2 by small-molecule inhibitors or genetic means enhanced HCC cell eradication by NK cells in a NKG2D ligand-dependent manner. Collectively, these results demonstrate that EZH2 inhibition enhances HCC eradication by NK cells and that EZH2 functions, in part, as an oncogene by inhibiting immune response.
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Russell‐Hallinan A, Watson CJ, Baugh JA. Epigenetics of Aberrant Cardiac Wound Healing. Compr Physiol 2018; 8:451-491. [DOI: 10.1002/cphy.c170029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Serroukh Y, Gu-Trantien C, Hooshiar Kashani B, Defrance M, Vu Manh TP, Azouz A, Detavernier A, Hoyois A, Das J, Bizet M, Pollet E, Tabbuso T, Calonne E, van Gisbergen K, Dalod M, Fuks F, Goriely S, Marchant A. The transcription factors Runx3 and ThPOK cross-regulate acquisition of cytotoxic function by human Th1 lymphocytes. eLife 2018; 7:30496. [PMID: 29488879 PMCID: PMC5844691 DOI: 10.7554/elife.30496] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 02/20/2018] [Indexed: 01/07/2023] Open
Abstract
Cytotoxic CD4 (CD4CTX) T cells are emerging as an important component of antiviral and antitumor immunity, but the molecular basis of their development remains poorly understood. In the context of human cytomegalovirus infection, a significant proportion of CD4 T cells displays cytotoxic functions. We observed that the transcriptional program of these cells was enriched in CD8 T cell lineage genes despite the absence of ThPOK downregulation. We further show that establishment of CD4CTX-specific transcriptional and epigenetic programs occurred in a stepwise fashion along the Th1-differentiation pathway. In vitro, prolonged activation of naive CD4 T cells in presence of Th1 polarizing cytokines led to the acquisition of perforin-dependent cytotoxic activity. This process was dependent on the Th1 transcription factor Runx3 and was limited by the sustained expression of ThPOK. This work elucidates the molecular program of human CD4CTX T cells and identifies potential targets for immunotherapy against viral infections and cancer.
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Affiliation(s)
- Yasmina Serroukh
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Chunyan Gu-Trantien
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | | | - Matthieu Defrance
- Laboratoire d'Epigénétique du Cancer, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Thien-Phong Vu Manh
- Centre d'Immunologie de Marseille-Luminy 13288, Aix Marseille Université UM2, Marseille, France
| | - Abdulkader Azouz
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Aurélie Detavernier
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Alice Hoyois
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Martin Bizet
- Laboratoire d'Epigénétique du Cancer, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Emeline Pollet
- Centre d'Immunologie de Marseille-Luminy 13288, Aix Marseille Université UM2, Marseille, France
| | - Tressy Tabbuso
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Emilie Calonne
- Laboratoire d'Epigénétique du Cancer, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Klaas van Gisbergen
- Department of Haematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Marc Dalod
- Centre d'Immunologie de Marseille-Luminy 13288, Aix Marseille Université UM2, Marseille, France
| | - François Fuks
- Laboratoire d'Epigénétique du Cancer, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Stanislas Goriely
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
| | - Arnaud Marchant
- Institute for Medical Immunology, Université Libre de Bruxelles, Charleroi, Belgium
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Origin and differentiation of human memory CD8 T cells after vaccination. Nature 2017; 552:362-367. [PMID: 29236685 DOI: 10.1038/nature24633] [Citation(s) in RCA: 354] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 10/13/2017] [Indexed: 02/06/2023]
Abstract
The differentiation of human memory CD8 T cells is not well understood. Here we address this issue using the live yellow fever virus (YFV) vaccine, which induces long-term immunity in humans. We used in vivo deuterium labelling to mark CD8 T cells that proliferated in response to the virus and then assessed cellular turnover and longevity by quantifying deuterium dilution kinetics in YFV-specific CD8 T cells using mass spectrometry. This longitudinal analysis showed that the memory pool originates from CD8 T cells that divided extensively during the first two weeks after infection and is maintained by quiescent cells that divide less than once every year (doubling time of over 450 days). Although these long-lived YFV-specific memory CD8 T cells did not express effector molecules, their epigenetic landscape resembled that of effector CD8 T cells. This open chromatin profile at effector genes was maintained in memory CD8 T cells isolated even a decade after vaccination, indicating that these cells retain an epigenetic fingerprint of their effector history and remain poised to respond rapidly upon re-exposure to the pathogen.
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Ochando J, Braza MS. T follicular helper cells: a potential therapeutic target in follicular lymphoma. Oncotarget 2017; 8:112116-112131. [PMID: 29340116 PMCID: PMC5762384 DOI: 10.18632/oncotarget.22788] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/20/2017] [Indexed: 12/30/2022] Open
Abstract
Follicular lymphoma (FL), the most common indolent B-cell non-Hodgkin lymphoma (B-NHL), is a germinal center (GC)-derived lymphoma. The mechanisms underlying B-cell differentiation/maturation in GCs could be also involved in their malignant transformation. Moreover, the non-malignant cell composition and architecture of the tumor microenvironment can influence FL development and outcome. Here, we review recent research advances on CD4 helper T cells in FL that highlight the pivotal role of T follicular helper (TFH) cells in a complex multicellular system where they interact with B cells during GC dynamics. After describing the mechanism of FL lymphomagenesis, we discuss the emerging evidence about TFH cell enrichment and involvement in FL tumorigenesis and in B-T cell interaction, TFH regulation by T follicular regulatory cells (TFR) and its potential effect on FL. Then, we provide an overview on the flexible interplay between the different CD4 T-cell subtypes and how this may be predicted in normal and pathologic contexts, according to the cell epigenetic state. Finally, we highlight the importance of targeting TFH cells in the clinic, summarize the main outstanding questions about TFH and TFR cells in FL, and describe strategies to potentiate FL therapy by taking into account TFH cells.
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Affiliation(s)
- Jordi Ochando
- Immunology Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mounia S Braza
- Immunology Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Ballestar E, Li T. New insights into the epigenetics of inflammatory rheumatic diseases. Nat Rev Rheumatol 2017; 13:593-605. [DOI: 10.1038/nrrheum.2017.147] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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